chr9-21202411-C-A

Variant names:

• chr9-21202411-C-A
• rs7045980
• NM_021057.2:c.-246G>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_021057.2(IFNA7):​c.-246G>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 151,026 control chromosomes in the GnomAD database, including 8,100 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.32 (8100 hom., cov: 31)
• Consequence: IFNA7 NM_021057.2 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

Genes affected

IFNA7 (HGNC:5428): (interferon alpha 7) Predicted to enable cytokine activity and type I interferon receptor binding activity. Predicted to be involved in several processes, including B cell activation; lymphocyte activation involved in immune response; and positive regulation of peptidyl-serine phosphorylation of STAT protein. Predicted to be located in extracellular region. Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IFNA7	NM_021057.2	c.-246G>T		upstream_gene_variant		ENST00000239347.3	NP_066401.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IFNA7	ENST00000239347.3	c.-246G>T		upstream_gene_variant		6	NM_021057.2	ENSP00000239347.3

Frequencies

GnomAD3 genomes AF: 0.324 AC: 48846 AN: 150906 Hom.: 8097 Cov.: 31

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.406

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.342

Gnomad OTH AF: 0.336

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.324 AC: 48869 AN: 151026 Hom.: 8100 Cov.: 31 AF XY: 0.326 AC XY: 24057 AN XY: 73718

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.310

Gnomad4 ASJ AF: 0.323

Gnomad4 EAS AF: 0.333

Gnomad4 SAS AF: 0.504

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.343

Gnomad4 OTH AF: 0.343

Alfa AF: 0.192 Hom.: 389

Bravo AF: 0.317

Asia WGS AF: 0.436 AC: 1517 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.054
DANN	Benign	0.31

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7045980; hg19: chr9-21202410; COSMIC: COSV53332223;